A function to retrieve collections from the Paleobiology Database (PBDB), matched to Macrostrat units.
get_fossils(
unit_id = NULL,
column_id = NULL,
interval_name = NULL,
age = NULL,
age_top = NULL,
age_bottom = NULL,
lithology = NULL,
lithology_id = NULL,
lithology_type = NULL,
lithology_class = NULL,
environ = NULL,
environ_id = NULL,
environ_type = NULL,
environ_class = NULL,
econ = NULL,
econ_id = NULL,
econ_type = NULL,
econ_class = NULL,
project_id = NULL,
strat_name_id = NULL,
sf = FALSE
)A dataframe containing the following columns:
collection_no: The unique identification number of the
collection, as assigned in the PBDB.
collection_name: The unique name of the collection, as
assigned in the PBDB.
t_age: The top age of the unit containing the collection,
estimated using the continuous time age model, in millions of years before
present.
b_age: The bottom age of the unit containing the collection,
estimated using the continuous time age model, in millions of years before
present.
pbdb_occs: The count of PBDB occurrences in the specified
PBDB collection.
genus_no: A vector containing the unique identification number
for each genus that appears in the collection, corresponding to the
genus_no column in the Paleobiology Database.
taxon_no: The count of unique taxa in the specified PBDB
collection.
unit_id: The unique identification number of the Macrostrat
unit containing the specified PBDB collection.
col_id: The unique identification number of the Macrostrat
column containing the specified PBDB collection.
refs: Reference for the source of the data.
strat_name_concept_id: The unique identification number of the
stratigraphic name concept containing the specified PBDB collection.
If sf = TRUE, an sf object is returned instead.
integer. Filter PBDB collections to those within one or
more unit(s) as specified by their unique identification number(s).
integer. Filter PBDB collections to those within one
or more column(s) as specified by their unique identification number(s).
character. Filter PBDB collections to those that
overlap with a named chronostratigraphic time interval (e.g., "Permian").
numeric. Filter PBDB collections to those that overlap with
the specified numerical age, in millions of years before present.
numeric. Filter PBDB collections to those that overlap
with the age range between the specified numerical age and age_bottom.
Should be in millions of years before present. age_bottom must also be
specified, and this must be older than age_top.
numeric. Filter PBDB collections to those that
overlap with the age range between the specified numerical age and
age_top. Should be in millions of years before present. age_top must
also be specified, and this must be younger than age_bottom.
character. Filter PBDB collections to those
containing a named lithology (e.g., "shale", "sandstone").
integer. Filter PBDB collections to those
containing one or more lithology(ies) identified by their unique
identification number(s).
character. Filter PBDB collections to those
containing a named lithology type (e.g., "carbonate", "siliciclastic").
character. Filter PBDB collections to those
containing a named lithology class (e.g., "sedimentary", "igneous",
"metamorphic").
character. Filter PBDB collections to those containing
a named environment (e.g., "delta plain", "pond").
integer. Filter PBDB collections to those containing
one or more environment(s) as specified by their unique identification
number(s).
character. Filter PBDB collections to those
containing a named environment type (e.g., "fluvial", "eolian", "glacial").
character. Filter PBDB collections to those
containing a named environment class (e.g., "marine", "non-marine").
character. Filter PBDB collections to those containing a
named economic attribute (e.g., "brick", "ground water", "gold").
integer. Filter PBDB collections to those containing
one or more economic attribute(s) as specified by their unique
identification number(s).
character. Filter PBDB collections to those
containing a named economic attribute type (e.g., "construction",
"aquifer", "mineral").
character. Filter PBDB collections to those
containing a named economic attribute class (e.g., "material", "water",
"precious commodity").
integer. Filter sections to those contained within a
Macrostrat project as specified by its unique identification number.
integer. Filter PBDB collections to those
containing a unit that matches one or more stratigraphic name(s) as
specified by their unique identification number(s).
logical. Should the results be returned as an sf object?
Defaults to FALSE.
Christopher D. Dean
Lewis A. Jones
More information can be found for the inputs for this function
using the definition functions (beginning with def_). Terminology
related to the PBDB can be found at https://paleobiodb.org/#/ or in
the suggested references below.
Peters, S.E. and McClennen, M. (2016). The Paleobiology Database application programming interface. Paleobiology, 42(1), pp. 1--7. tools:::Rd_expr_doi("10.1017/pab.2015.39").
Uhen, M.D., Allen, B., Behboudi, N., Clapham, M.E., Dunne, E., Hendy, A., Holroyd, P.A., Hopkins, M., Mannion, P., Novack-Gottshall, P. and Pimiento, C. (2023). Paleobiology Database User Guide Version 1.0. PaleoBios, 40(11), pp. 1--56. tools:::Rd_expr_doi("10.5070/P9401160531").
External data:
def_drilling_sites(),
def_measurements(),
get_eodp(),
get_measurements()
# \donttest{
# Get fossils by Macrostrat column ID
ex1 <- get_fossils(column_id = 10)
# Get fossils by Macrostrat unit ID
ex2 <- get_fossils(unit_id = 6279)
# Get fossils by lithology and age
ex3 <- get_fossils(lithology = "sandstone", age_top = 66, age_bottom = 73)
# Get fossils by environment type and age
ex4 <- get_fossils(environ_type = "fluvial", age = 253)
# }
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